That ibdata1 isn't shrinking is a particularly annoying feature of MySQL. The ibdata1 file can´t actually be shrunk unless you delete all databases, remove the files and reload a dump. But you can configure MySQL so that each table, including its indexes, is stored as a separate file. In that way ibdata1 will not grow as large. According to Bill Karwin's comment this is enabled by default as of version 5.6 of MySQL. It was a while ago I did this. However, to setup your server to use separate files for each table you need to change my.cnf in order to enable this: [mysqld] innodb_file_per_table http://dev.mysql.com/doc/refman/5.5/en/innodb-multiple-tablespaces.html As you want to reclaim the space from ibdata1 you actually have to delete the file: Do a mysqldump of all databases, procedures, triggers etc except the mysql and performance_schema databases Drop all databases except the above 2 databases Stop mysql Delete ibdata1 and ib_log files Start mysql Restore from dump When you start MySQL in step 5 the ibdata1 and ib_log files will be recreated. Now you're fit to go. When you create a new database for analysis, the tables will be located in separate ibd* files, not in ibdata1. As you usually drop the database soon after, the ibd* files will be deleted. http://dev.mysql.com/doc/refman/5.1/en/drop-database.html You have probably seen this: http://bugs.mysql.com/bug.php?id=1341 By using the command ALTER TABLE
ENGINE=innodb or OPTIMIZE TABLE one can extract data and index pages from ibdata1 to separate files. However, ibdata1 will not shrink unless you do the steps above.